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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
5dt9NADErythronate-4-phosphate dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5dt9NADErythronate-4-phosphate dehydrogenase/1.000
3oetNADErythronate-4-phosphate dehydrogenase/0.535
4zgsNADPutative D-lactate dehydrogenase/0.497
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.495
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.489
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.487
4b65FADL-ornithine N(5)-monooxygenase/0.483
3atzFMNProstaglandin F2a synthase/0.481
2eklNADD-3-phosphoglycerate dehydrogenase/0.475
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.475
2cy0NAPShikimate dehydrogenase (NADP(+))/0.470
1psdNADD-3-phosphoglycerate dehydrogenase1.1.1.950.468
4ebfNADPhosphonate dehydrogenase1.20.1.10.468
1ybaNADD-3-phosphoglycerate dehydrogenase1.1.1.950.466
2ylrNAPPhenylacetone monooxygenase1.14.13.920.465
1j49NADD-lactate dehydrogenase1.1.1.280.464
4y7cNAPNADPH--cytochrome P450 reductase/0.464
4q72FADBifunctional protein PutA/0.463
4y9uNAPNADPH--cytochrome P450 reductase/0.462
3kb1ADPIron-sulfur cluster carrier protein/0.461
4q73FADBifunctional protein PutA/0.461
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.460
1bwsNDPGDP-L-fucose synthase/0.459
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.458
2nv6ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
3h4lANPDNA mismatch repair protein PMS1/0.458
3ksdNADGlyceraldehyde-3-phosphate dehydrogenase 1/0.458
4jicFMNGTN Reductase/0.458
4q71FADBifunctional protein PutA/0.458
2ohvNHLGlutamate racemase/0.456
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.456
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
3gobHXXDdmC/0.454
4ejmNAPPutative zinc-binding dehydrogenase/0.454
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.452
1nytNAPShikimate dehydrogenase (NADP(+))/0.452
4i1iNADMalate dehydrogenase/0.452
4a99FADTetX family tetracycline inactivation enzyme/0.451
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.450
1nzdUPGDNA beta-glucosyltransferase/0.450
4y9rNAPNADPH--cytochrome P450 reductase/0.450
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1u4oNDDL-lactate dehydrogenase1.1.1.270.449
2d8aNADL-threonine 3-dehydrogenase/0.449
2ok7FADFerredoxin--NADP reductase, apicoplast/0.449
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
5d3qGDPDynamin-13.6.5.50.449
1e3eNAIAlcohol dehydrogenase 41.1.1.10.448
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
4b68FADL-ornithine N(5)-monooxygenase/0.448
2x0rNADMalate dehydrogenase/0.447
3copADPGlycogen synthase2.4.1.210.447
4tqgNDPPutative dTDP-d-glucose 4 6-dehydratase/0.446
4yaw2AMNADPH--cytochrome P450 reductase/0.446
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.446
5kgpACOPredicted acetyltransferase/0.446
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.445
1m13HYFNuclear receptor subfamily 1 group I member 2/0.444
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.444
2oapANPType II secretion system protein (GspE-2)/0.444
2uzfCAA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.444
2wq7FADRE11660p/0.444
3f03FMNPentaerythritol tetranitrate reductase/0.444
1enyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
1h51FMNPentaerythritol tetranitrate reductase/0.443
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
2bpoNAPNADPH--cytochrome P450 reductase/0.443
2ejvNADL-threonine 3-dehydrogenase/0.443
2q7vFADThioredoxin reductase/0.443
3p62FMNPentaerythritol tetranitrate reductase/0.443
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4jhz1KVBeta-glucuronidase3.2.1.310.443
1adfTADAlcohol dehydrogenase E chain1.1.1.10.442
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
3gfbNADL-threonine 3-dehydrogenase/0.442
4e2bFMNDehydrogenase/0.442
2hs8FMN12-oxophytodienoate reductase 31.3.1.420.441
3atyFMNProstaglandin F2a synthase/0.441
3lqfNADGalactitol dehydrogenase/0.441
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.441
4nxuADPMitochondrial dynamics protein MID51/0.441
4o3mADPBloom syndrome protein3.6.4.120.441
2wq6FADRE11660p/0.440
3a4vNADNDP-sugar epimerase/0.440